All-atom MD simulation of Mycoplasma cytoplasm
Villin Crowding System
Replica Exchange Umbrella Sampling
What is GENESIS?
- GENESIS (GENeralized-Ensemble SImulation System) has been developed mainly by Sugita group in RIKEN, (Computational Biophysics Research Team (R-CCS), Theoretical Molecular Science Laboratory (CPR), and Laboratory for Biomolecular Function Simulation (BDR)) since 2009.
- Using GENESIS, molecular dynamics simulation and modeling of various biomolecular systems are possible with high performance.
- Multi-scale simulations with atomistic, coarse-grained, and QM/MM models are available together with enhanced sampling methods and other advanced simulation techniques.
- GENESIS (version 1.5 or later) is free software under the LGPLv3. Earlier versions (<=1.4) were distributed as free software under the GPLv2 license.
Functions of GENESIS
The GENESIS package contains two MD programs (
spdyn), trajectory analysis programs, and other useful tools.
- CHARMM force field, AMBER force field, MARTINI model, Go models (Cα Go, all-atom Go, KB Go, and AICG2+), and residue-level coarse-grained DNA/RNA models
- Energy minimization and molecular dynamics simulations
- Leapfrog, velocity Verlet, and RESPA integrators
- SHAKE/RATTLE, SETTLE, and LINCS algorithms for bond constraint
- Bussi, Langevin, and Berendsen thermostat/barostat in the NVT, NPT, NPAT, and NPγT ensembles
- Replica-exchange molecular dynamics method (REMD) in temperature, pressure, and surface-tension space
- Generalized replica-exchange with solute tempering (gREST)
- Replica-exchange umbrella sampling (REUS) with collective variables
- Multi-dimensional REMD method (T-REMD/P-REMD, T-REMD/REUS, gREST/REUS, etc)
- Gaussian accelerated molecular dynamics method (GaMD, GaREUS)
- String method for reaction pathway search
- Hybrid QM/MM (quantum mechanics/molecular mechanics) calculation
- Implicit solvent model (Generalized Born/Solvent Accessible Surface Area model)
- Cryo-EM flexible fitting using all-atom, CG, and implicit solvent models with MD, REMD, and REUS
- Free-energy perturbation method (FEP)
- Anharmonic vibrational analysis using SINDO
- Steered MD and Targeted MD simulations
- Restrained MD simulations (Distance, angle, dihedral angle, position, etc)
- Hybrid MPI+OpenMP, hybrid CPU+GPGPU, mixed double+single precision calculations
- Highly-parallelized Particle mesh Ewald method (PME)
- Scalable MD simulations for huge systems (> 100,000,000 atoms)
- Trajectory analysis tools (RMSD, RMSF, PCA, WHAM, MBAR, etc.)
- Spatial decomposition analysis (SPANA)
MD trajectories obtained by GENESIS can be visualized with VMD and other software. CHARMM-GUI input generator can be used for the preparation of GENESIS input files.
How to cite GENESIS
See this page.